snoweye/phyclust: Phylogenetic Clustering (Phyloclustering)

Version 0.1-23

Phylogenetic clustering (phyloclustering) is an evolutionary
Continuous Time Markov Chain model-based approach to identify
population structure from molecular data without assuming
linkage equilibrium. The package phyclust (Chen 2011) provides a
convenient implementation of phyloclustering for DNA and SNP data,
capable of clustering individuals into subpopulations and identifying
molecular sequences representative of those subpopulations. It is
designed in C for performance, interfaced with R for visualization,
and incorporates other popular open source programs including
ms (Hudson 2002) ,
seq-gen (Rambaut and Grassly 1997)
,
Hap-Clustering (Tzeng 2005) and
PAML baseml (Yang 1997, 2007) ,
,
for simulating data, additional analyses, and searching the best tree.
See the phyclust website for more information, documentations and
examples.